Polyphenol-protein interactions are crucial for food processing, nutrition, and functional properties. This study investigates the interaction between rutin and β-casein (β-CAS) or β-lactoglobulin (β-LG) using multispectral analysis, molecular docking, and molecular dynamics (MD) simulations. Fluorescence spectroscopy reveals that rutin binds spontaneously (ΔG <
0) to β-CAS and β-LG, forming complexes with binding constants (Ka) at 298 K of 42.500 × 10